In [2]:
import sys
import modeller
import _modeller
import modeller.automodel
from IPython.display import Image
In [3]:
#Зададим параметры
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.24, 2020/04/06, r11614
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2020 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux kodomo 3.16.0-6-amd64 x86_64
Date and time of compilation : 2020/04/06 19:06:24
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2020/05/21 18:10:48
In [3]:
#Скачаем белок заготовку P50718
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2020-05-21 16:54:47-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 128.6.244.52 Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following] --2020-05-21 16:54:47-- https://www.rcsb.org/pdb/files/1lmp.pdb Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65 Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected. ERROR: The certificate of `www.rcsb.org' is not trusted. ERROR: The certificate of `www.rcsb.org' hasn't got a known issuer.
In [23]:
#Скачаем последовательность лизоцима мотылька
! wget http://www.uniprot.org/uniprot/P50718.fasta
--2020-05-21 17:57:56-- http://www.uniprot.org/uniprot/Q7SID7.fasta Resolving www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.192.81 Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org:443/uniprot/Q7SID7.fasta [following] --2020-05-21 17:57:57-- https://www.uniprot.org/uniprot/Q7SID7.fasta Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... connected. HTTP request sent, awaiting response... 200 Length: 192 [text/plain] Saving to: `Q7SID7.fasta' 100%[======================================>] 192 --.-K/s in 0s 2020-05-21 17:57:58 (84.5 MB/s) - `Q7SID7.fasta' saved [192/192]
In [13]:
#Создадим объект выравнивание
alignm=modeller.alignment(env)
In [14]:
alignm.append(file='P50718.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'LYS_TRINI'
alignm[1].code = '1lmp'
In [15]:
#Делаем выравнивание и сохраняем
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [16]:
! cat all_in_one.ali
>P1;LYS_TRINI sequence:: : : : :::-1.00:-1.00 MQKLRVFLLALAALCISCEAKYFATNCELVHELRRQGFPEDKMRDWVCLIQNESGRNTSKMGTINKNGSRDYGLF QINDKYWCSKTSTPGKD--CNVTCAEMLLDDITKASKCAKKI-YKRHKFQAWYGWRNHCQGTLPDISKC------ -* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELA------------------RALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIF QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV.. .*
С выравнивамнием кажется все ок¶
In [17]:
# Выбираем объект для моделирования.
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
# Создаем объект automodel.
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
LYS_TRINI 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
92 1 73 76 D C 8.895
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 11787 10783
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 141
Number of all, selected real atoms : 1135 1135
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10783 10783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2431
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1088.7938
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1158 0 1 0.008 0.008 18.820 1.000
2 Bond angle potential : 1555 1 12 2.360 2.360 171.60 1.000
3 Stereochemical cosine torsion poten: 730 0 31 47.208 47.208 261.01 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.449 1.449 20.379 1.000
5 Soft-sphere overlap restraints : 2431 0 0 0.003 0.003 2.4318 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2217 0 1 0.402 0.402 119.41 1.000
10 Distance restraints 2 (N-O) : 2375 0 5 0.438 0.438 148.40 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 1 3 5.382 5.382 47.829 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 0 68.060 68.060 37.037 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 2 78.053 78.053 46.700 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 1 82.328 82.328 31.651 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 97.542 97.542 16.162 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.24811 1.000
19 Disulfide angle restraints : 6 0 0 2.102 2.102 0.58517 1.000
20 Disulfide dihedral angle restraints: 3 0 0 29.779 29.779 2.4403 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1244 0 0 0.417 0.417 25.421 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 139 16 25 31.678 63.832 109.21 1.000
26 Distance restraints 4 (SDCH-SDCH) : 459 0 0 0.695 0.695 29.468 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_TRINI.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16661.7832
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2164 92D 92D N CA 731 732 123.73 107.00 16.73 4.81 107.00 16.73 4.81
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4103 38F 38F CA C 296 304 -154.45 -180.00 25.55 5.11 -180.00 25.55 5.11
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3935 9L 10A C N 78 80 51.08 -68.20 120.46 10.75 -62.50 -166.26 29.20
1 10A 10A N CA 80 81 162.14 145.30 -40.90
2 3936 10A 11L C N 83 85 -121.99 -108.50 29.63 1.43 -63.50 170.28 27.26
2 11L 11L N CA 85 86 158.88 132.50 -41.20
3 3937 11L 12A C N 91 93 -85.00 -68.20 40.72 3.82 -62.50 150.79 23.71
3 12A 12A N CA 93 94 108.20 145.30 -40.90
4 3938 12A 13A C N 96 98 -148.57 -134.00 20.83 0.64 -62.50 179.23 33.97
4 13A 13A N CA 98 99 161.89 147.00 -40.90
5 3939 13A 14L C N 101 103 -102.43 -108.50 11.19 0.64 -63.50 -178.87 27.53
5 14L 14L N CA 103 104 141.90 132.50 -41.20
6 3942 16I 17S C N 123 125 -70.61 -72.40 4.14 0.30 -64.10 168.99 12.64
6 17S 17S N CA 125 126 156.13 152.40 -35.00
7 3945 19E 20A C N 144 146 -173.53 -134.00 40.40 1.66 -62.50 -148.86 31.66
7 20A 20A N CA 146 147 138.69 147.00 -40.90
8 3946 20A 21K C N 149 151 -175.90 -118.00 57.96 2.14 -62.90 -149.58 34.04
8 21K 21K N CA 151 152 141.70 139.10 -40.80
9 3947 21K 22Y C N 158 160 -129.49 -124.30 22.38 1.41 -63.50 170.33 24.12
9 22Y 22Y N CA 160 161 113.63 135.40 -43.40
10 3948 22Y 23F C N 170 172 -136.65 -124.20 75.05 3.81 -63.20 135.27 15.28
10 23F 23F N CA 172 173 69.29 143.30 -44.30
11 3950 24A 25T C N 186 188 -86.77 -78.10 30.18 1.05 -63.20 141.18 19.68
11 25T 25T N CA 188 189 178.71 149.80 -42.10
12 3951 25T 26N C N 193 195 -97.06 -71.20 51.68 2.76 -63.20 135.65 18.89
12 26N 26N N CA 195 196 -172.45 142.80 -41.10
13 3953 27C 28E C N 207 209 -71.27 -63.60 49.20 6.99 -63.60 49.20 6.99
13 28E 28E N CA 209 210 -88.90 -40.30 -40.30
14 4011 85K 86T C N 689 691 81.27 55.90 51.01 2.46 -124.80 -146.29 12.84
14 86T 86T N CA 691 692 -4.75 39.50 143.50
15 4017 91K 92D C N 729 731 -137.01 -63.30 80.35 13.69 -63.30 80.35 13.69
15 92D 92D N CA 731 732 -71.96 -40.00 -40.00
16 4041 115I 116Y C N 906 908 -51.50 -98.40 49.49 2.61 -63.50 156.47 25.44
16 116Y 116Y N CA 908 909 112.60 128.40 -43.40
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 19 55 72 120 127 152 147 193 186
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 141
Number of all, selected real atoms : 1135 1135
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10783 10783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2395
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1207.7847
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1158 0 1 0.008 0.008 22.665 1.000
2 Bond angle potential : 1555 1 10 2.468 2.468 186.73 1.000
3 Stereochemical cosine torsion poten: 730 0 28 48.315 48.315 269.61 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.496 1.496 21.989 1.000
5 Soft-sphere overlap restraints : 2395 0 0 0.003 0.003 2.9229 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2217 0 4 0.380 0.380 116.96 1.000
10 Distance restraints 2 (N-O) : 2375 0 15 0.435 0.435 178.40 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 1 4 5.378 5.378 47.751 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 4 75.428 75.428 49.875 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 77.352 77.352 45.785 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 85.939 85.939 29.554 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 74.928 74.928 17.158 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.25617 1.000
19 Disulfide angle restraints : 6 0 0 3.006 3.006 1.1967 1.000
20 Disulfide dihedral angle restraints: 3 0 0 26.437 26.437 2.0178 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1244 0 0 0.485 0.485 32.536 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 139 23 28 30.723 73.130 132.90 1.000
26 Distance restraints 4 (SDCH-SDCH) : 459 0 0 0.869 0.869 49.490 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_TRINI.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 18093.2266
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2164 92D 92D N CA 731 732 124.06 107.00 17.06 4.91 107.00 17.06 4.91
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4103 38F 38F CA C 296 304 -156.52 -180.00 23.48 4.69 -180.00 23.48 4.69
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3935 9L 10A C N 78 80 140.47 -134.00 85.72 2.62 -62.50 -131.26 45.52
1 10A 10A N CA 80 81 152.77 147.00 -40.90
2 3937 11L 12A C N 91 93 158.63 -134.00 71.13 1.67 -62.50 -156.11 40.53
2 12A 12A N CA 93 94 169.82 147.00 -40.90
3 3938 12A 13A C N 96 98 -96.85 -68.20 30.02 2.81 -62.50 -179.45 28.11
3 13A 13A N CA 98 99 136.35 145.30 -40.90
4 3939 13A 14L C N 101 103 -104.98 -108.50 9.17 0.45 -63.50 170.36 21.65
4 14L 14L N CA 103 104 124.03 132.50 -41.20
5 3940 14L 15C C N 109 111 36.73 -69.10 121.54 11.29 -117.90 166.03 6.68
5 15C 15C N CA 111 112 -158.44 141.80 141.10
6 3942 16I 17S C N 123 125 -84.38 -72.40 27.81 1.30 -64.10 148.89 12.11
6 17S 17S N CA 125 126 177.50 152.40 -35.00
7 3945 19E 20A C N 144 146 -83.60 -68.20 15.54 1.38 -62.50 177.12 30.11
7 20A 20A N CA 146 147 143.24 145.30 -40.90
8 3946 20A 21K C N 149 151 -122.62 -118.00 8.40 0.32 -62.90 -176.90 27.34
8 21K 21K N CA 151 152 146.12 139.10 -40.80
9 3947 21K 22Y C N 158 160 -100.92 -98.40 8.60 0.89 -63.50 -176.18 31.09
9 22Y 22Y N CA 160 161 136.63 128.40 -43.40
10 3948 22Y 23F C N 170 172 -87.48 -71.40 22.81 2.00 -63.20 170.57 22.10
10 23F 23F N CA 172 173 124.53 140.70 -44.30
11 3949 23F 24A C N 181 183 -165.31 -134.00 35.05 0.80 -62.50 -172.85 36.12
11 24A 24A N CA 183 184 162.73 147.00 -40.90
12 3950 24A 25T C N 186 188 -66.83 -78.10 16.81 0.60 -63.20 179.46 22.78
12 25T 25T N CA 188 189 137.32 149.80 -42.10
13 3951 25T 26N C N 193 195 -125.42 -119.90 15.58 0.57 -63.20 178.53 25.86
13 26N 26N N CA 195 196 151.57 137.00 -41.10
14 3961 35R 36Q C N 280 282 -62.66 -63.80 1.17 0.20 -121.10 -171.00 7.85
14 36Q 36Q N CA 282 283 -40.04 -40.30 139.70
15 3962 36Q 37G C N 289 291 -86.08 -62.40 28.07 4.22 82.20 171.81 12.61
15 37G 37G N CA 291 292 -26.13 -41.20 8.50
16 3979 53E 54S C N 433 435 -137.34 -64.10 78.57 8.64 -64.10 78.57 8.64
16 54S 54S N CA 435 436 -6.56 -35.00 -35.00
17 4011 85K 86T C N 689 691 77.88 55.90 46.01 2.20 -124.80 -146.45 12.87
17 86T 86T N CA 691 692 -0.92 39.50 143.50
18 4017 91K 92D C N 729 731 -136.72 -63.30 79.29 13.50 -63.30 79.29 13.50
18 92D 92D N CA 731 732 -69.95 -40.00 -40.00
19 4041 115I 116Y C N 906 908 -48.57 -98.40 52.60 2.78 -63.50 155.67 25.47
19 116Y 116Y N CA 908 909 111.55 128.40 -43.40
20 4044 118R 119H C N 938 940 -92.35 -125.60 70.92 2.01 -63.20 121.99 13.68
20 119H 119H N CA 940 941 76.15 138.80 -42.30
21 4045 119H 120K C N 948 950 -60.91 -62.90 31.39 3.97 -118.00 159.34 8.23
21 120K 120K N CA 950 951 -72.13 -40.80 139.10
22 4055 129N 130H C N 1045 1047 -119.51 -63.20 73.77 8.59 -63.20 73.77 8.59
22 130H 130H N CA 1047 1048 5.35 -42.30 -42.30
23 4056 130H 131C C N 1055 1057 -121.66 -63.00 60.52 9.18 -63.00 60.52 9.18
23 131C 131C N CA 1057 1058 -26.24 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 10 15 58 61 120 118 136 169 175 188
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_TRINI.B99990001.pdb 1088.79382
LYS_TRINI.B99990002.pdb 1207.78467
In [32]:
#Визуализируем модель 1
Image("Lysosim.png", width = 700)
Out[32]:
In [33]:
#Визуализируем модель 2
Image("Lysosim2.png", width = 700)
Out[33]:
Видим, что структуры получились довольно похожие, выделяется длинная петля у анализируемой последовательности¶
Добавим лиганд к новой структуре¶
In [18]:
seq_liganded = ''
for res in alignm[0].residues:
seq_liganded += res.code
for lig in alignm[1].residues[-3:]:
seq_liganded += lig.code
alignm.append_sequence(seq_liganded)
alignm[2].code = 'LYS_TRINI_withlig'
del alignm[0]
In [19]:
# Делаем выравнивание.
alignm.salign()
# Сохраняем в файл.
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [20]:
# Смотрим на выравнивание.
! cat all_in_one2.ali
>P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELA------------------RALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIF QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV.. .* >P1;LYS_TRINI_withlig sequence::1 : :+144 : :undefined:undefined:-1.00:-1.00 MQKLRVFLLALAALCISCEAKYFATNCELVHELRRQGFPEDKMRDWVCLIQNESGRNTSKMGTINKNGSRDYGLF QINDKYWCSKTSTPGKD--CNVTCAEMLLDDITKASKCAKKI-YKRHKFQAWYGWRNHCQG----TLPDISKC.. .*
In [21]:
# выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
# создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
92 1 73 76 D C 8.895
136 1 117 122 G T 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C +N
atom indices : 1133 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C CA +N O
atom indices : 1133 1130 0 1134
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13130 12126
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12126 12126
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2686
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1423.5923
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1158 0 1 0.009 0.009 28.607 1.000
2 Bond angle potential : 1555 2 13 2.533 2.533 198.01 1.000
3 Stereochemical cosine torsion poten: 730 0 39 49.961 49.961 285.10 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.645 1.645 26.244 1.000
5 Soft-sphere overlap restraints : 2686 1 2 0.008 0.008 21.658 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2202 0 8 0.519 0.519 190.41 1.000
10 Distance restraints 2 (N-O) : 2360 0 13 0.549 0.549 211.56 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 1 6 5.712 5.712 53.874 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 5 81.850 81.850 51.516 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 77.914 77.914 41.901 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 78.563 78.563 28.440 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 92.985 92.985 17.043 1.000
18 Disulfide distance restraints : 3 0 0 0.019 0.019 0.19031 1.000
19 Disulfide angle restraints : 6 0 0 3.736 3.736 1.8492 1.000
20 Disulfide dihedral angle restraints: 3 0 0 43.872 43.872 4.1162 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1225 0 0 0.385 0.385 22.829 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 139 24 35 35.659 73.818 176.06 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 0 0 0.762 0.762 37.510 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.048 0.048 26.659 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 19517.2773
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1447 28E 28E N CA 209 210 126.52 107.00 19.52 5.61 107.00 19.52 5.61
2 2164 92D 92D N CA 731 732 124.52 107.00 17.52 5.04 107.00 17.52 5.04
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4103 38F 38F CA C 296 304 -156.98 -180.00 23.02 4.60 -180.00 23.02 4.60
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3935 9L 10A C N 78 80 63.08 -68.20 131.59 10.85 -62.50 -142.76 42.23
1 10A 10A N CA 80 81 136.37 145.30 -40.90
2 3936 10A 11L C N 83 85 -137.65 -108.50 29.34 1.44 -63.50 -174.21 22.86
2 11L 11L N CA 85 86 129.15 132.50 -41.20
3 3937 11L 12A C N 91 93 -70.16 -68.20 3.99 0.38 -62.50 177.44 29.46
3 12A 12A N CA 93 94 141.83 145.30 -40.90
4 3938 12A 13A C N 96 98 -157.49 -134.00 27.87 0.67 -62.50 -176.40 35.15
4 13A 13A N CA 98 99 161.99 147.00 -40.90
5 3939 13A 14L C N 101 103 -85.26 -70.70 22.81 1.43 -63.50 161.11 23.67
5 14L 14L N CA 103 104 159.16 141.60 -41.20
6 3942 16I 17S C N 123 125 -73.28 -72.40 3.21 0.22 -64.10 175.92 13.31
6 17S 17S N CA 125 126 149.31 152.40 -35.00
7 3944 18C 19E C N 135 137 -58.51 -69.30 11.35 0.73 -63.60 179.34 24.19
7 19E 19E N CA 137 138 138.96 142.50 -40.30
8 3945 19E 20A C N 144 146 -65.03 -68.20 6.68 0.44 -62.50 179.70 29.57
8 20A 20A N CA 146 147 139.42 145.30 -40.90
9 3946 20A 21K C N 149 151 -123.80 -118.00 5.80 0.22 -62.90 -170.16 22.13
9 21K 21K N CA 151 152 139.00 139.10 -40.80
10 3948 22Y 23F C N 170 172 -118.64 -124.20 5.62 0.24 -63.20 -179.70 28.72
10 23F 23F N CA 172 173 144.13 143.30 -44.30
11 3949 23F 24A C N 181 183 -171.70 -134.00 37.79 1.16 -62.50 -158.35 38.84
11 24A 24A N CA 183 184 149.58 147.00 -40.90
12 3950 24A 25T C N 186 188 -140.24 -124.80 22.81 1.36 -63.20 -174.43 19.89
12 25T 25T N CA 188 189 126.71 143.50 -42.10
13 3953 27C 28E C N 207 209 -83.91 -63.60 49.53 7.74 -63.60 49.53 7.74
13 28E 28E N CA 209 210 -85.47 -40.30 -40.30
14 4011 85K 86T C N 689 691 76.17 55.90 44.51 2.13 -124.80 -145.71 12.92
14 86T 86T N CA 691 692 -0.13 39.50 143.50
15 4017 91K 92D C N 729 731 -146.87 -63.30 90.90 15.49 -63.30 90.90 15.49
15 92D 92D N CA 731 732 -75.77 -40.00 -40.00
16 4043 117K 118R C N 927 929 -59.72 -125.20 81.90 2.42 -63.00 132.55 18.13
16 118R 118R N CA 929 930 91.41 140.60 -41.10
17 4044 118R 119H C N 938 940 177.19 -63.20 121.42 18.12 -63.20 121.42 18.12
17 119H 119H N CA 940 941 -21.45 -42.30 -42.30
18 4045 119H 120K C N 948 950 51.91 -70.20 145.11 12.02 -118.00 -172.32 8.57
18 120K 120K N CA 950 951 -141.20 140.40 139.10
19 4055 129N 130H C N 1045 1047 -124.35 -63.20 71.25 8.96 -63.20 71.25 8.96
19 130H 130H N CA 1047 1048 -5.73 -42.30 -42.30
20 4058 132Q 133G C N 1070 1072 131.50 78.70 57.45 2.17 82.20 170.07 10.62
20 133G 133G N CA 1072 1073 171.27 -166.10 8.50
21 4059 133G 134T C N 1074 1076 -112.94 -124.80 38.21 1.31 -63.20 157.34 17.39
21 134T 134T N CA 1076 1077 107.17 143.50 -42.10
22 4061 135L 136P C N 1089 1091 -76.26 -64.50 35.16 3.26 -58.70 145.63 10.67
22 136P 136P N CA 1091 1092 114.07 147.20 -30.50
23 4062 136P 137D C N 1096 1098 -77.99 -70.90 60.52 2.64 -63.30 110.57 14.57
23 137D 137D N CA 1098 1099 -149.59 150.30 -40.00
24 4065 139S 140K C N 1118 1120 55.58 56.60 5.13 0.30 -62.90 145.48 25.28
24 140K 140K N CA 1120 1121 43.63 38.60 -40.80
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 15 21 86 101 153 134 144 180 206 203
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12126 12126
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2564
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1353.4377
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1158 0 1 0.009 0.009 29.351 1.000
2 Bond angle potential : 1555 2 14 2.501 2.501 190.45 1.000
3 Stereochemical cosine torsion poten: 730 0 30 49.230 49.230 277.39 1.000
4 Stereochemical improper torsion pot: 471 0 0 1.338 1.338 18.055 1.000
5 Soft-sphere overlap restraints : 2564 2 2 0.008 0.008 21.745 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2202 1 9 0.503 0.503 182.85 1.000
10 Distance restraints 2 (N-O) : 2360 0 11 0.534 0.534 216.93 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 2 5 5.835 5.835 56.212 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 1 81.029 81.029 41.756 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 68.389 68.389 40.154 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 78.250 78.250 29.326 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 86.360 86.360 15.054 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.31572 1.000
19 Disulfide angle restraints : 6 0 0 3.273 3.273 1.4193 1.000
20 Disulfide dihedral angle restraints: 3 0 0 28.228 28.228 1.7621 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1225 0 0 0.439 0.439 27.915 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 139 23 30 32.740 76.348 135.07 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 0 0 0.731 0.731 37.322 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.052 0.052 30.356 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 19216.9336
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2164 92D 92D N CA 731 732 123.93 107.00 16.93 4.87 107.00 16.93 4.87
2 2653 135L 135L N CA 1083 1084 122.72 107.00 15.72 4.52 107.00 15.72 4.52
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4103 38F 38F CA C 296 304 -155.55 -180.00 24.45 4.89 -180.00 24.45 4.89
2 4199 134T 134T CA C 1077 1081 -156.90 -180.00 23.10 4.62 -180.00 23.10 4.62
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3935 9L 10A C N 78 80 179.81 -134.00 46.23 1.60 -62.50 -149.97 40.65
1 10A 10A N CA 80 81 145.14 147.00 -40.90
2 3936 10A 11L C N 83 85 -167.51 -108.50 59.80 2.97 -63.50 -165.81 23.86
2 11L 11L N CA 85 86 122.79 132.50 -41.20
3 3937 11L 12A C N 91 93 -166.06 -134.00 36.73 0.85 -62.50 -174.28 35.92
3 12A 12A N CA 93 94 164.93 147.00 -40.90
4 3938 12A 13A C N 96 98 -127.56 -134.00 8.13 0.45 -62.50 179.35 32.87
4 13A 13A N CA 98 99 151.97 147.00 -40.90
5 3939 13A 14L C N 101 103 -94.10 -108.50 25.79 1.21 -63.50 155.35 20.03
5 14L 14L N CA 103 104 111.11 132.50 -41.20
6 3942 16I 17S C N 123 125 -62.63 -72.40 15.89 1.24 -64.10 160.07 11.51
6 17S 17S N CA 125 126 164.94 152.40 -35.00
7 3944 18C 19E C N 135 137 -89.38 -69.30 26.87 2.47 -63.60 166.95 20.95
7 19E 19E N CA 137 138 124.64 142.50 -40.30
8 3947 21K 22Y C N 158 160 -133.67 -124.30 15.49 0.63 -63.50 -177.13 32.51
8 22Y 22Y N CA 160 161 147.73 135.40 -43.40
9 3948 22Y 23F C N 170 172 -125.76 -124.20 10.91 0.55 -63.20 -172.45 22.32
9 23F 23F N CA 172 173 132.51 143.30 -44.30
10 3949 23F 24A C N 181 183 -132.70 -134.00 12.36 0.67 -62.50 -170.88 28.51
10 24A 24A N CA 183 184 134.71 147.00 -40.90
11 3950 24A 25T C N 186 188 -111.05 -124.80 14.71 0.63 -63.20 -174.10 27.03
11 25T 25T N CA 188 189 138.26 143.50 -42.10
12 3951 25T 26N C N 193 195 -123.31 -119.90 7.27 0.39 -63.20 -178.10 20.07
12 26N 26N N CA 195 196 130.58 137.00 -41.10
13 3989 63T 64I C N 503 505 -63.43 -63.40 12.87 2.11 -120.60 170.88 7.72
13 64I 64I N CA 505 506 -30.73 -43.60 130.30
14 4011 85K 86T C N 689 691 80.54 55.90 48.65 2.35 -124.80 -147.36 12.80
14 86T 86T N CA 691 692 -2.45 39.50 143.50
15 4017 91K 92D C N 729 731 -138.24 -63.30 80.63 13.71 -63.30 80.63 13.71
15 92D 92D N CA 731 732 -69.75 -40.00 -40.00
16 4041 115I 116Y C N 906 908 -49.64 -98.40 54.98 3.47 -63.50 147.05 24.05
16 116Y 116Y N CA 908 909 102.99 128.40 -43.40
17 4044 118R 119H C N 938 940 -86.96 -125.60 53.36 1.32 -63.20 146.24 16.93
17 119H 119H N CA 940 941 102.00 138.80 -42.30
18 4056 130H 131C C N 1055 1057 -76.95 -63.00 79.79 10.75 -63.00 79.79 10.75
18 131C 131C N CA 1057 1058 -119.66 -41.10 -41.10
19 4058 132Q 133G C N 1070 1072 109.68 78.70 64.24 0.96 82.20 132.01 7.75
19 133G 133G N CA 1072 1073 137.62 -166.10 8.50
20 4059 133G 134T C N 1074 1076 140.13 -63.20 160.17 26.55 -63.20 160.17 26.55
20 134T 134T N CA 1076 1077 -75.37 -42.10 -42.10
21 4062 136P 137D C N 1096 1098 36.17 -70.90 122.88 10.31 -63.30 147.86 16.41
21 137D 137D N CA 1098 1099 -149.40 150.30 -40.00
22 4064 138I 139S C N 1112 1114 -132.79 -136.60 47.60 2.33 -64.10 154.83 9.84
22 139S 139S N CA 1114 1115 103.75 151.20 -35.00
23 4065 139S 140K C N 1118 1120 -57.74 -70.20 28.66 1.80 -62.90 155.47 20.48
23 140K 140K N CA 1120 1121 114.58 140.40 -40.80
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 13 16 66 84 132 139 134 174 202 204
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_TRINI_withlig.B99990001.pdb 1423.59229
LYS_TRINI_withlig.B99990002.pdb 1353.43774
In [22]:
#Визуализируем модель 1 с лигандом
Image("Lysosim_lig.png", width = 700)
Out[22]:
In [23]:
#Визуализируем модель 2 с лигандом
Image("Lysosim_lig2.png", width = 700)
Out[23]:
Видим, что молекулы лигандов совпали¶
Передвинем лиганд в другое место¶
In [36]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('O:123','CA:114')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
In [37]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
92 1 73 76 D C 8.895
136 1 117 122 G T 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C +N
atom indices : 1133 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 141
atom names : C CA +N O
atom indices : 1133 1130 0 1134
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13131 12127
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12127 12127
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2646
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1959.1710
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1158 0 1 0.010 0.010 36.531 1.000
2 Bond angle potential : 1555 3 19 2.707 2.707 219.74 1.000
3 Stereochemical cosine torsion poten: 730 0 43 50.675 50.675 286.04 1.000
4 Stereochemical improper torsion pot: 471 1 3 1.769 1.769 36.262 1.000
5 Soft-sphere overlap restraints : 2646 1 3 0.009 0.009 24.258 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2202 8 28 0.646 0.646 337.79 1.000
10 Distance restraints 2 (N-O) : 2360 6 30 0.659 0.659 367.59 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 1 10 6.388 6.388 67.362 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 2 77.924 77.924 49.748 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 73.267 73.267 44.583 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 81.976 81.976 30.666 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 82.889 82.889 14.456 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.25096 1.000
19 Disulfide angle restraints : 6 0 0 2.276 2.276 0.68613 1.000
20 Disulfide dihedral angle restraints: 3 0 0 18.572 18.572 1.0851 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1225 0 0 0.451 0.451 34.984 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 139 27 35 39.965 74.508 240.73 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 0 2 0.982 0.982 55.439 1.000
27 Distance restraints 5 (X-Y) : 1390 1 5 0.078 0.078 110.97 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 20360.7461
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2164 92D 92D N CA 731 732 124.25 107.00 17.25 4.96 107.00 17.25 4.96
2 2653 135L 135L N CA 1083 1084 123.29 107.00 16.29 4.69 107.00 16.29 4.69
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3854 123A 123A C CA 982 980 13.23 0.00 13.23 4.66 0.00 13.23 4.66
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8755 122Q 115I N O 970 907 10.87 7.52 3.35 4.65 7.52 3.35 4.65
2 8773 123A 115I N O 979 907 10.12 6.71 3.41 5.82 6.71 3.41 5.82
3 8796 124W 115I N O 984 907 10.84 7.90 2.94 5.21 7.90 2.94 5.21
4 8819 125Y 123A N O 998 983 5.38 3.62 1.76 4.84 3.62 1.76 4.84
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3935 9L 10A C N 78 80 -148.12 -134.00 15.60 0.35 -62.50 -173.69 35.11
1 10A 10A N CA 80 81 153.63 147.00 -40.90
2 3936 10A 11L C N 83 85 -68.89 -70.70 1.82 0.16 -63.50 177.46 24.95
2 11L 11L N CA 85 86 141.42 141.60 -41.20
3 3937 11L 12A C N 91 93 -95.77 -68.20 40.23 3.96 -62.50 160.39 24.87
3 12A 12A N CA 93 94 116.00 145.30 -40.90
4 3938 12A 13A C N 96 98 -134.11 -134.00 10.24 0.58 -62.50 177.00 32.84
4 13A 13A N CA 98 99 157.24 147.00 -40.90
5 3942 16I 17S C N 123 125 -130.02 -136.60 18.21 0.76 -64.10 -178.39 11.23
5 17S 17S N CA 125 126 134.22 151.20 -35.00
6 3945 19E 20A C N 144 146 -103.24 -134.00 33.05 0.76 -62.50 -179.53 27.87
6 20A 20A N CA 146 147 134.91 147.00 -40.90
7 3947 21K 22Y C N 158 160 -37.05 -98.40 64.47 2.98 -63.50 170.44 25.73
7 22Y 22Y N CA 160 161 148.22 128.40 -43.40
8 3948 22Y 23F C N 170 172 -58.83 -71.40 20.82 1.85 -63.20 158.47 21.71
8 23F 23F N CA 172 173 157.29 140.70 -44.30
9 3949 23F 24A C N 181 183 -135.01 -134.00 23.51 1.31 -62.50 165.37 30.98
9 24A 24A N CA 183 184 170.48 147.00 -40.90
10 3950 24A 25T C N 186 188 -70.34 -78.10 23.13 1.25 -63.20 146.48 19.26
10 25T 25T N CA 188 189 171.59 149.80 -42.10
11 3953 27C 28E C N 207 209 -101.78 -63.60 39.88 6.74 -63.60 39.88 6.74
11 28E 28E N CA 209 210 -51.80 -40.30 -40.30
12 3961 35R 36Q C N 280 282 -58.73 -63.80 6.22 1.13 -121.10 -172.92 7.67
12 36Q 36Q N CA 282 283 -36.68 -40.30 139.70
13 3962 36Q 37G C N 289 291 -87.37 -62.40 27.21 4.31 82.20 173.97 12.86
13 37G 37G N CA 291 292 -30.37 -41.20 8.50
14 3979 53E 54S C N 433 435 -135.30 -64.10 77.09 8.36 -64.10 77.09 8.36
14 54S 54S N CA 435 436 -5.43 -35.00 -35.00
15 4011 85K 86T C N 689 691 76.84 55.90 46.57 2.22 -124.80 -144.89 12.96
15 86T 86T N CA 691 692 -2.09 39.50 143.50
16 4017 91K 92D C N 729 731 -142.08 -63.30 84.19 14.30 -63.30 84.19 14.30
16 92D 92D N CA 731 732 -69.69 -40.00 -40.00
17 4038 112A 113K C N 880 882 -69.42 -118.00 76.68 2.82 -62.90 120.75 15.34
17 113K 113K N CA 882 883 79.78 139.10 -40.80
18 4039 113K 114K C N 889 891 32.05 -62.90 127.23 15.79 -62.90 127.23 15.79
18 114K 114K N CA 891 892 -125.49 -40.80 -40.80
19 4041 115I 116Y C N 906 908 87.39 -124.30 156.09 12.80 -63.50 -160.73 37.72
19 116Y 116Y N CA 908 909 86.75 135.40 -43.40
20 4048 122Q 123A C N 977 979 -74.01 -62.50 80.31 12.65 -62.50 80.31 12.65
20 123A 123A N CA 979 980 38.58 -40.90 -40.90
21 4055 129N 130H C N 1045 1047 -128.15 -63.20 82.05 9.75 -63.20 82.05 9.75
21 130H 130H N CA 1047 1048 7.84 -42.30 -42.30
22 4056 130H 131C C N 1055 1057 -103.19 -63.00 86.92 9.02 -63.00 86.92 9.02
22 131C 131C N CA 1057 1058 35.98 -41.10 -41.10
23 4057 131C 132Q C N 1061 1063 -70.81 -63.80 15.16 2.59 -121.10 173.98 8.92
23 132Q 132Q N CA 1063 1064 -53.75 -40.30 139.70
24 4058 132Q 133G C N 1070 1072 17.53 78.70 61.17 3.09 82.20 -173.59 12.10
24 133G 133G N CA 1072 1073 -166.33 -166.10 8.50
25 4059 133G 134T C N 1074 1076 -148.30 -124.80 63.64 3.40 -63.20 152.42 16.11
25 134T 134T N CA 1076 1077 84.35 143.50 -42.10
26 4062 136P 137D C N 1096 1098 44.27 -70.90 126.33 10.58 -63.30 159.50 17.72
26 137D 137D N CA 1098 1099 -157.77 150.30 -40.00
27 4065 139S 140K C N 1118 1120 58.56 56.60 7.43 0.68 -62.90 149.15 25.91
27 140K 140K N CA 1120 1121 45.77 38.60 -40.80
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12127 123A 114K O CA 983 892 4.45 3.00 1.45 14.46 3.00 1.45 14.46
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 2 17 22 86 82 135 133 172 171 175 206
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 144
Number of all, selected real atoms : 1178 1178
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12127 12127
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2740
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 2088.0029
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1158 0 1 0.011 0.011 42.199 1.000
2 Bond angle potential : 1555 3 21 2.704 2.704 225.53 1.000
3 Stereochemical cosine torsion poten: 730 0 40 51.338 51.338 297.48 1.000
4 Stereochemical improper torsion pot: 471 0 2 1.858 1.858 39.909 1.000
5 Soft-sphere overlap restraints : 2740 1 2 0.010 0.010 31.486 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2202 8 26 0.663 0.663 374.49 1.000
10 Distance restraints 2 (N-O) : 2360 2 31 0.656 0.656 374.58 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 140 6 11 7.820 7.820 100.95 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 2 77.530 77.530 44.268 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 2 78.126 78.126 42.676 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 89.166 89.166 32.997 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 95.519 95.519 12.958 1.000
18 Disulfide distance restraints : 3 0 0 0.021 0.021 0.21848 1.000
19 Disulfide angle restraints : 6 0 0 2.054 2.054 0.55892 1.000
20 Disulfide dihedral angle restraints: 3 0 0 39.182 39.182 3.0534 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1225 0 0 0.481 0.481 38.015 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 139 29 33 38.524 79.112 228.97 1.000
26 Distance restraints 4 (SDCH-SDCH) : 462 0 0 1.010 1.010 59.121 1.000
27 Distance restraints 5 (X-Y) : 1390 1 6 0.085 0.085 138.55 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 21648.9297
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1480 31H 31H N CA 233 234 123.38 107.00 16.38 4.71 107.00 16.38 4.71
2 2164 92D 92D N CA 731 732 126.74 107.00 19.74 5.68 107.00 19.74 5.68
3 2393 115I 115I N CA 900 901 123.31 107.00 16.31 4.69 107.00 16.31 4.69
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8819 125Y 123A N O 998 983 5.38 3.62 1.76 4.83 3.62 1.76 4.83
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4103 38F 38F CA C 296 304 -152.13 -180.00 27.87 5.57 -180.00 27.87 5.57
2 4178 113K 113K CA C 883 889 -154.49 -180.00 25.51 5.10 -180.00 25.51 5.10
3 4180 115I 115I CA C 901 906 -150.75 -180.00 29.25 5.85 -180.00 29.25 5.85
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3935 9L 10A C N 78 80 -78.72 -68.20 23.90 1.58 -62.50 153.20 25.93
1 10A 10A N CA 80 81 166.76 145.30 -40.90
2 3936 10A 11L C N 83 85 -78.20 -70.70 22.63 1.47 -63.50 156.54 22.61
2 11L 11L N CA 85 86 162.95 141.60 -41.20
3 3937 11L 12A C N 91 93 -115.16 -134.00 20.80 1.03 -62.50 171.57 30.92
3 12A 12A N CA 93 94 155.82 147.00 -40.90
4 3938 12A 13A C N 96 98 -56.30 -68.20 26.69 1.76 -62.50 162.43 26.93
4 13A 13A N CA 98 99 121.42 145.30 -40.90
5 3939 13A 14L C N 101 103 -133.34 -108.50 25.13 1.16 -63.50 -169.22 23.58
5 14L 14L N CA 103 104 136.34 132.50 -41.20
6 3942 16I 17S C N 123 125 -116.50 -136.60 44.06 1.72 -64.10 156.05 9.62
6 17S 17S N CA 125 126 111.99 151.20 -35.00
7 3944 18C 19E C N 135 137 -141.01 -117.80 23.50 0.78 -63.60 -164.82 30.37
7 19E 19E N CA 137 138 140.53 136.80 -40.30
8 3945 19E 20A C N 144 146 -128.30 -134.00 7.91 0.46 -62.50 179.14 32.88
8 20A 20A N CA 146 147 152.48 147.00 -40.90
9 3948 22Y 23F C N 170 172 84.96 -124.20 150.95 6.06 -63.20 -128.36 26.27
9 23F 23F N CA 172 173 137.64 143.30 -44.30
10 3949 23F 24A C N 181 183 -135.74 -134.00 15.83 0.93 -62.50 -172.91 28.15
10 24A 24A N CA 183 184 131.26 147.00 -40.90
11 3950 24A 25T C N 186 188 -123.84 -124.80 9.35 0.37 -63.20 -173.56 20.54
11 25T 25T N CA 188 189 134.20 143.50 -42.10
12 3951 25T 26N C N 193 195 -124.42 -119.90 28.36 1.18 -63.20 165.63 24.18
12 26N 26N N CA 195 196 165.00 137.00 -41.10
13 3956 30V 31H C N 231 233 178.75 -125.60 70.19 3.14 -63.20 -178.14 19.92
13 31H 31H N CA 233 234 96.03 138.80 -42.30
14 3964 38F 39P C N 304 306 -19.92 -58.70 44.10 4.11 -64.50 167.36 14.91
14 39P 39P N CA 306 307 -51.48 -30.50 147.20
15 3965 39P 40E C N 311 313 -153.77 -117.80 100.62 5.49 54.60 151.63 17.86
15 40E 40E N CA 313 314 42.84 136.80 42.40
16 3979 53E 54S C N 433 435 -137.73 -64.10 82.25 8.55 -64.10 82.25 8.55
16 54S 54S N CA 435 436 1.65 -35.00 -35.00
17 3989 63T 64I C N 503 505 -63.12 -63.40 13.49 2.22 -120.60 170.41 7.68
17 64I 64I N CA 505 506 -30.12 -43.60 130.30
18 4011 85K 86T C N 689 691 75.19 55.90 26.34 1.64 -124.80 -158.82 12.20
18 86T 86T N CA 691 692 21.56 39.50 143.50
19 4012 86T 87S C N 696 698 -141.39 -64.10 91.49 8.85 -64.10 91.49 8.85
19 87S 87S N CA 698 699 13.95 -35.00 -35.00
20 4017 91K 92D C N 729 731 179.64 -96.50 93.31 3.80 -63.30 162.89 18.52
20 92D 92D N CA 731 732 73.28 114.20 -40.00
21 4038 112A 113K C N 880 882 -60.66 -118.00 71.55 2.42 -62.90 137.12 17.93
21 113K 113K N CA 882 883 96.30 139.10 -40.80
22 4041 115I 116Y C N 906 908 14.70 -98.40 123.76 7.30 -63.50 144.54 26.61
22 116Y 116Y N CA 908 909 78.15 128.40 -43.40
23 4048 122Q 123A C N 977 979 -72.13 -62.50 74.70 11.81 -62.50 74.70 11.81
23 123A 123A N CA 979 980 33.18 -40.90 -40.90
24 4055 129N 130H C N 1045 1047 -122.21 -63.20 69.25 8.66 -63.20 69.25 8.66
24 130H 130H N CA 1047 1048 -6.06 -42.30 -42.30
25 4058 132Q 133G C N 1070 1072 131.14 78.70 56.86 2.17 82.20 170.58 10.63
25 133G 133G N CA 1072 1073 171.92 -166.10 8.50
26 4059 133G 134T C N 1074 1076 -113.17 -124.80 33.59 1.13 -63.20 161.98 17.96
26 134T 134T N CA 1076 1077 111.98 143.50 -42.10
27 4061 135L 136P C N 1089 1091 -78.83 -64.50 33.36 3.25 -58.70 148.94 10.76
27 136P 136P N CA 1091 1092 117.08 147.20 -30.50
28 4062 136P 137D C N 1096 1098 -78.93 -70.90 60.64 2.60 -63.30 110.71 14.65
28 137D 137D N CA 1098 1099 -149.60 150.30 -40.00
29 4065 139S 140K C N 1118 1120 57.87 56.60 2.62 0.28 -62.90 145.81 25.38
29 140K 140K N CA 1120 1121 40.89 38.60 -40.80
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12127 123A 114K O CA 983 892 4.65 3.00 1.65 16.54 3.00 1.65 16.54
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 13 29 95 79 144 156 162 192 191 201
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_TRINI_withlig.B99990001.pdb 1959.17102
LYS_TRINI_withlig.B99990002.pdb 2088.00293
In [42]:
Image("Lysosim_moved1.png", width = 700)
Out[42]:
In [43]:
Image("Lysosim_moved.png", width = 700)
Out[43]:
Видно, по коричневым и бирюзовым шарикам, что положение лиганда сместилось, хотя и не сильно.¶
Заменим все аминокислоты на Ala¶
In [45]:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
ala_prot = 'A' * 120 + '...'
alignm.append_sequence(ala_prot)
alignm[0].code = 'pdb'
alignm[1].code = 'ala_changed'
In [46]:
alignm.salign()
alignm.write(file='align_ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [47]:
! cat align_ala.ali
>P1;pdb structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;ala_changed sequence::1 : :+123 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA---------AAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
In [48]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_ala.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
ala_changed pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
55 1 55 65 A A 16.730
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C +N
atom indices : 599 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C CA +N O
atom indices : 599 597 0 600
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 8748 8155
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 644 644
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8155 8155
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1131
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1149.6335
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 600 0 1 0.008 0.008 12.594 1.000
2 Bond angle potential : 839 0 5 2.294 2.294 91.242 1.000
3 Stereochemical cosine torsion poten: 244 0 30 74.546 74.546 221.70 1.000
4 Stereochemical improper torsion pot: 240 0 0 0.986 0.986 6.0719 1.000
5 Soft-sphere overlap restraints : 1131 1 2 0.011 0.011 16.749 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 1968 8 30 0.807 0.807 289.51 1.000
10 Distance restraints 2 (N-O) : 2093 7 34 0.779 0.779 392.30 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 119 0 5 5.513 5.513 42.649 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 668 0 0 0.283 0.283 5.9001 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 118 18 17 31.178 65.702 51.578 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.007 1.007 4.0650 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.037 0.037 15.270 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: ala_changed.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 11512.1084
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3583 56A 63A CA CA 277 312 13.26 7.04 6.22 5.87 7.04 6.22 5.87
2 3584 56A 64A CA CA 277 317 13.71 7.69 6.02 4.69 7.69 6.02 4.69
3 3585 56A 65A CA CA 277 322 10.91 5.45 5.47 6.29 5.45 5.47 6.29
4 3588 56A 68A CA CA 277 337 12.20 7.46 4.74 4.60 7.46 4.74 4.60
5 3589 56A 69A CA CA 277 342 10.10 6.07 4.03 5.66 6.07 4.03 5.66
6 3590 56A 70A CA CA 277 347 9.93 4.69 5.24 7.48 4.69 5.24 7.48
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4905 38A 55A N O 186 275 8.42 5.51 2.91 4.97 5.51 2.91 4.97
2 5216 56A 63A N O 276 315 13.95 7.89 6.07 4.92 7.89 6.07 4.92
3 5217 56A 64A N O 276 320 13.15 7.21 5.93 4.51 7.21 5.93 4.51
4 5218 56A 65A N O 276 325 13.40 6.37 7.03 6.65 6.37 7.03 6.65
5 5221 56A 68A N O 276 340 12.57 7.02 5.55 5.18 7.02 5.55 5.18
6 5222 56A 69A N O 276 345 8.95 2.70 6.25 12.21 2.70 6.25 12.21
7 5389 71A 56A N O 351 280 6.09 2.97 3.11 6.58 2.97 3.11 6.58
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1938 15A 16A C N 74 76 79.55 55.40 27.79 2.07 -62.50 156.37 31.76
1 16A 16A N CA 76 77 24.46 38.20 -40.90
2 1941 18A 19A C N 89 91 64.96 55.40 18.81 0.71 -62.50 142.13 28.89
2 19A 19A N CA 91 92 22.00 38.20 -40.90
3 1943 20A 21A C N 99 101 61.99 -68.20 146.26 14.16 -62.50 164.25 25.83
3 21A 21A N CA 101 102 -148.04 145.30 -40.90
4 1944 21A 22A C N 104 106 -108.73 -134.00 87.19 4.23 -62.50 114.22 17.17
4 22A 22A N CA 106 107 63.55 147.00 -40.90
5 1945 22A 23A C N 109 111 -71.36 -62.50 10.50 2.13 -134.00 177.86 10.95
5 23A 23A N CA 111 112 -46.53 -40.90 147.00
6 1959 36A 37A C N 179 181 66.14 55.40 13.59 0.85 -62.50 146.82 29.86
6 37A 37A N CA 181 182 29.87 38.20 -40.90
7 1960 37A 38A C N 184 186 60.60 55.40 8.45 0.37 -62.50 142.83 29.04
7 38A 38A N CA 186 187 31.54 38.20 -40.90
8 1971 48A 49A C N 239 241 83.70 55.40 37.50 2.18 -62.50 156.02 31.57
8 49A 49A N CA 241 242 13.59 38.20 -40.90
9 1980 57A 58A C N 284 286 56.09 55.40 8.55 0.57 -62.50 147.45 29.87
9 58A 58A N CA 286 287 46.72 38.20 -40.90
10 1984 61A 62A C N 304 306 57.67 55.40 6.13 0.23 -62.50 140.82 28.63
10 62A 62A N CA 306 307 32.50 38.20 -40.90
11 1986 63A 64A C N 314 316 -77.90 -68.20 10.90 0.75 -62.50 169.54 28.57
11 64A 64A N CA 316 317 150.26 145.30 -40.90
12 1987 64A 65A C N 319 321 -85.37 -68.20 37.84 3.58 -62.50 154.19 24.25
12 65A 65A N CA 321 322 111.58 145.30 -40.90
13 1989 66A 67A C N 329 331 -94.83 -68.20 51.08 4.91 -62.50 146.24 22.61
13 67A 67A N CA 331 332 101.72 145.30 -40.90
14 1990 67A 68A C N 334 336 -60.72 -68.20 39.47 2.92 -62.50 147.46 24.25
14 68A 68A N CA 336 337 106.55 145.30 -40.90
15 2017 94A 95A C N 469 471 79.52 -134.00 160.77 3.65 -62.50 177.12 28.38
15 95A 95A N CA 471 472 -146.73 147.00 -40.90
16 2030 107A 108A C N 534 536 53.77 55.40 2.67 0.12 -62.50 141.82 28.77
16 108A 108A N CA 536 537 40.32 38.20 -40.90
17 2039 116A 117A C N 579 581 66.39 55.40 36.39 1.42 -62.50 136.32 27.54
17 117A 117A N CA 581 582 3.51 38.20 -40.90
18 2041 118A 119A C N 589 591 133.04 -134.00 131.18 3.94 -62.50 -177.30 37.13
18 119A 119A N CA 591 592 -120.45 147.00 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 4 4 37 48 66 53 82 95 102 64
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 644 644
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8155 8155
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1129
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1163.4586
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 600 0 1 0.008 0.008 11.742 1.000
2 Bond angle potential : 839 0 4 2.217 2.217 85.320 1.000
3 Stereochemical cosine torsion poten: 244 0 33 76.196 76.196 232.32 1.000
4 Stereochemical improper torsion pot: 240 0 0 0.920 0.920 5.0349 1.000
5 Soft-sphere overlap restraints : 1129 1 2 0.011 0.011 15.941 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 1968 7 25 0.796 0.796 290.74 1.000
10 Distance restraints 2 (N-O) : 2093 8 34 0.769 0.769 337.75 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 119 0 3 4.891 4.891 33.575 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 668 0 0 0.390 0.390 11.102 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 118 25 19 41.468 77.990 110.87 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.380 1.380 7.0948 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.046 0.046 21.968 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: ala_changed.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 12193.0361
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3583 56A 63A CA CA 277 312 12.36 7.04 5.31 5.02 7.04 5.31 5.02
2 3584 56A 64A CA CA 277 317 13.94 7.69 6.25 4.87 7.69 6.25 4.87
3 3585 56A 65A CA CA 277 322 11.74 5.45 6.29 7.23 5.45 6.29 7.23
4 3588 56A 68A CA CA 277 337 12.27 7.46 4.81 4.67 7.46 4.81 4.67
5 3589 56A 69A CA CA 277 342 9.90 6.07 3.82 5.37 6.07 3.82 5.37
6 3590 56A 70A CA CA 277 347 8.84 4.69 4.15 5.92 4.69 4.15 5.92
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4905 38A 55A N O 186 275 8.23 5.51 2.73 4.65 5.51 2.73 4.65
2 5216 56A 63A N O 276 315 13.86 7.89 5.97 4.85 7.89 5.97 4.85
3 5218 56A 65A N O 276 325 11.23 6.37 4.86 4.59 6.37 4.86 4.59
4 5220 56A 67A N O 276 335 12.43 7.89 4.53 4.51 7.89 4.53 4.51
5 5221 56A 68A N O 276 340 12.92 7.02 5.89 5.50 7.02 5.89 5.50
6 5222 56A 69A N O 276 345 8.34 2.70 5.64 11.02 2.70 5.64 11.02
7 5389 71A 56A N O 351 280 5.75 2.97 2.78 5.87 2.97 2.78 5.87
8 5427 73A 70A N O 361 350 6.04 3.17 2.86 4.65 3.17 2.86 4.65
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1925 2A 3A C N 9 11 -63.15 -62.50 9.77 1.63 -68.20 164.13 13.42
1 3A 3A N CA 11 12 -50.65 -40.90 145.30
2 1926 3A 4A C N 14 16 24.70 -68.20 102.96 7.15 -68.20 102.96 7.15
2 4A 4A N CA 16 17 100.91 145.30 145.30
3 1938 15A 16A C N 74 76 78.10 55.40 25.92 1.96 -62.50 155.56 31.61
3 16A 16A N CA 76 77 25.68 38.20 -40.90
4 1941 18A 19A C N 89 91 64.57 55.40 20.47 0.74 -62.50 140.86 28.63
4 19A 19A N CA 91 92 19.89 38.20 -40.90
5 1943 20A 21A C N 99 101 53.81 55.40 4.19 0.38 -62.50 138.51 28.14
5 21A 21A N CA 101 102 34.33 38.20 -40.90
6 1944 21A 22A C N 104 106 62.95 55.40 10.71 0.56 -62.50 144.39 29.37
6 22A 22A N CA 106 107 30.60 38.20 -40.90
7 1959 36A 37A C N 179 181 66.20 55.40 14.95 0.81 -62.50 145.91 29.67
7 37A 37A N CA 181 182 27.86 38.20 -40.90
8 1960 37A 38A C N 184 186 55.70 55.40 1.33 0.10 -62.50 142.95 29.02
8 38A 38A N CA 186 187 39.50 38.20 -40.90
9 1971 48A 49A C N 239 241 154.76 -134.00 73.14 1.87 -62.50 -148.88 41.93
9 49A 49A N CA 241 242 163.55 147.00 -40.90
10 1972 49A 50A C N 244 246 90.05 -134.00 136.20 4.21 -68.20 158.55 13.77
10 50A 50A N CA 246 247 155.19 147.00 145.30
11 1976 53A 54A C N 264 266 58.16 -68.20 144.29 14.03 -62.50 159.39 25.06
11 54A 54A N CA 266 267 -145.04 145.30 -40.90
12 1979 56A 57A C N 279 281 -160.68 -134.00 28.40 1.32 -62.50 -156.57 30.47
12 57A 57A N CA 281 282 137.27 147.00 -40.90
13 1980 57A 58A C N 284 286 -66.00 -68.20 5.56 0.37 -62.50 178.94 29.50
13 58A 58A N CA 286 287 140.20 145.30 -40.90
14 1983 60A 61A C N 299 301 -64.51 -62.50 2.97 0.59 -68.20 171.66 13.98
14 61A 61A N CA 301 302 -43.08 -40.90 145.30
15 1986 63A 64A C N 314 316 -66.45 -68.20 7.11 0.63 -62.50 166.96 27.56
15 64A 64A N CA 316 317 152.19 145.30 -40.90
16 1988 65A 66A C N 324 326 78.44 -62.50 148.77 26.22 -62.50 148.77 26.22
16 66A 66A N CA 326 327 -88.52 -40.90 -40.90
17 1990 67A 68A C N 334 336 77.41 55.40 31.74 1.63 -62.50 150.78 30.56
17 68A 68A N CA 336 337 15.33 38.20 -40.90
18 1992 69A 70A C N 344 346 -66.93 -62.50 20.03 3.52 -134.00 166.66 10.28
18 70A 70A N CA 346 347 -60.43 -40.90 147.00
19 1993 70A 71A C N 349 351 -168.27 -62.50 105.96 20.10 -62.50 105.96 20.10
19 71A 71A N CA 351 352 -34.66 -40.90 -40.90
20 2017 94A 95A C N 469 471 80.49 -134.00 159.80 3.63 -62.50 178.02 28.54
20 95A 95A N CA 471 472 -146.94 147.00 -40.90
21 2030 107A 108A C N 534 536 106.01 -134.00 157.40 4.31 -62.50 -177.44 31.50
21 108A 108A N CA 536 537 -111.14 147.00 -40.90
22 2031 108A 109A C N 539 541 -159.63 -134.00 64.82 2.89 -68.20 110.04 7.23
22 109A 109A N CA 541 542 -153.47 147.00 145.30
23 2038 115A 116A C N 574 576 58.77 -68.20 134.11 12.63 -68.20 134.11 12.63
23 116A 116A N CA 576 577 -171.52 145.30 145.30
24 2039 116A 117A C N 579 581 -81.63 -68.20 72.72 6.33 -62.50 116.31 18.22
24 117A 117A N CA 581 582 73.83 145.30 -40.90
25 2041 118A 119A C N 589 591 65.72 55.40 13.90 0.79 -62.50 145.97 29.69
25 119A 119A N CA 591 592 28.89 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 3 6 38 52 65 68 75 97 96 77
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ala_changed.B99990001.pdb 1149.63354
ala_changed.B99990002.pdb 1163.45862
In [51]:
#Визуализируем аланины 1
Image("Ala1.png", width = 700)
Out[51]:
In [52]:
#Визуализируем аланины 2
Image("Ala2.png", width = 700)
Out[52]:
